scholarly journals Drought tolerance molecular responses of two cultivated varieties Jerusalem artichoke (Helianthus tuberosus L.) as revealed by RNA-Seq

2020 ◽  
Author(s):  
Shipeng Yang ◽  
Lihui Wang ◽  
Qiwen Zhong ◽  
Guangnan Zhang ◽  
Haiwang Zhang ◽  
...  
Keyword(s):  
Drought Stress ◽  
Drought Resistance ◽  
Metabolic Pathways ◽  
Jerusalem Artichoke ◽  
Tibet Plateau ◽  
Helianthus Tuberosus ◽  
Rna Seq ◽  
Concentration Gradients ◽  
Light Reaction ◽  
Metabolic Activities

Abstract Background Jerusalem artichoke (Helianthus tuberosus L.) is a highly stress-resistant crop, especially it grows normally in the desertified land of Qinghai-Tibet Plateau in the past two years, and has become a crop with agricultural, industrial and ecological functions. However, there are few studies on drought resistance of Jerusalem artichoke at present, and studies on the mechanisms of stress resistance of Jerusalem artichoke breeding and fructan are seriously lagging behind. In this study, we selected two differentially resistant cultivars for drought stress experiments with different concentration gradients, the aim was finding DEGs and metabolic pathways associated with drought stress. Results Based on an additional analysis of the metabolic pathways under drought stress using MapMan, the most different types of metabolism included secondary metabolism, light reaction metabolism and cell wall. As a whole, QY1 and QY3 both had a large number of up-regulated genes in the flavor pathway. It was suggested that flavonoids could help Jerusalem artichoke to resist drought stress and maintain normal metabolic activities. In addition, the gene analysis of the abscisic acid (ABA) key metabolic pathway showed that QY3 had more genes in NAC and WRKY than QY1, but QY1 had more genes in response to drought stress as a whole. By combining RNA-Seq and WGCNA, a weighted gene co-expression network was constructed and divided into modules. By analyzing specifically the expressed modules, four modules were found to have the highest correlation with drought. Further research on the genes revealed that all 16 genes related to histone, ABA and protein kinase had the highest significance in these pathways. Conclusions These findings represent the first RNA-Seq analysis of drought stress in Jerusalem artichoke, which is of substantial significance to explore the function of drought resistance in Jerusalem artichoke and the excavation of related genes.

scholarly journals Transcriptome changes induced by drought stress in Jerusalem artichoke (Helianthus tuberosus L.) and weighted gene co-expression network analysis (WGCNA)

2020 ◽  
Author(s):  
Shipeng Yang ◽  
Lihui Wang ◽  
Qiwen Zhong ◽  
Guangnan Zhang ◽  
Dengshan Zhang ◽  
...  
Keyword(s):  
Drought Stress ◽  
Drought Resistance ◽  
Jerusalem Artichoke ◽  
Northern China ◽  
Qinghai Lake ◽  
Helianthus Tuberosus ◽  
Rna Seq ◽  
Light Reaction ◽  
Qinghai Province ◽  
Watering Treatment

Abstract Background: Jerusalem artichoke (Helianthus tuberosus L.) is strongly resistant to stress and an important plant used for ecological management in northern China in recent years. Currently, Jerusalem artichoke has been widely planted in the area around Qinghai Lake in Qinghai Province, China. Jerusalem artichoke can not only prevent land desertification but also has maintain most of its level of production. However, there is little research on the mechanism of drought resistance of Jerusalem artichoke.Results: We conducted transcriptome sequencing under drought stress and normal watering treatment for two varieties, QY1 and QY3, with differing degrees of drought tolerance. In the three stress periods of QY1 and QY3, 5,613, 12,985 and 24,923 differentially expressed genes (DEGs) were identified, respectively. GO analysis showed that there were more DEGs in QY1 than in QY3, but there were more up-regulated genes in QY3 than in QY1. Based on an additional analysis of the metabolic pathways under drought stress using MapMan, the most different types of metabolism included secondary metabolism, light reaction metabolism and cell wall. The up-regulated genes in QY3 were significantly more prevalent than those in QY1 and were primarily concentrated in flavor IDS, phenylpropanoids, and the shikimate and terpenoids pathway. As a whole, QY1 and QY3 both had a large number of up-regulated genes in the flavor pathway. In addition, the gene analysis of the ABA key metabolic pathway showed that QY3 had more genes in NAC and WRKY than QY1. A weighted gene co-expression network was constructed and divided into modules. By specifically analyzing the expressed modules, four modules were found to have the highest correlation with drought. Further research on the genes revealed that all 16 genes related to histone, ABA and protein kinase were the most significant in these pathways.Conclusions: In summary, these findings represent the first RNA-Seq analysis of drought stress in Jerusalem artichoke, which is of substantial significance to explore the function of drought resistance in Jerusalem artichoke and the unearthing of related genes.

scholarly journals RNA-Seq Analysis and De Novo Transcriptome Assembly of Jerusalem Artichoke (Helianthus tuberosus Linne)

PLoS ONE ◽  
2014 ◽  
Vol 9 (11) ◽  
pp. e111982 ◽  
Author(s):  
Won Yong Jung ◽  
Sang Sook Lee ◽  
Chul Wook Kim ◽  
Hyun-Soon Kim ◽  
Sung Ran Min ◽  
...  
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Jerusalem Artichoke ◽  
Helianthus Tuberosus ◽  
De Novo Transcriptome Assembly ◽  
Rna Seq ◽  
De Novo Transcriptome

scholarly journals Expression of Genes Related to Plant Hormone Signal Transduction in Jerusalem artichoke (Helianthus tuberosus L.) Seedlings Under Salt Stress

2021 ◽  
Author(s):  
Yue Yang ◽  
Wang Jueyun ◽  
Ren Wencai ◽  
Zhaosheng Zhou ◽  
Long Xiaohua ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Abscisic Acid ◽  
Salt Stress ◽  
Plant Hormone ◽  
Jerusalem Artichoke ◽  
Helianthus Tuberosus ◽  
Rna Seq ◽  
Tolerance Mechanisms ◽  
Expression Of Genes ◽  
Gene Functions

Background: Jerusalem artichoke (Helianthus tuberosus L.) is tolerant to salinity stress and has high economic value. The salt tolerance mechanisms of Jerusalem artichoke are still unclear. Especially in the early stage of Jerusalem artichoke exposure to salt stress, the plant physiology, biochemistry and gene transcription are likely to undergo large changes. Elucidating these changes may be of great significance to understanding the salt tolerance mechanisms of it. Results: We obtained high-quality transcriptome from leaves and roots of Jerusalem artichoke exposed to salinity (300 mM NaCl) for 0 h, 6 h, 12 h, 24 h and 48 h, with 150,129 unigenes and 9023 DEGs (Differentially Expressed Genes). The RNA-seq data were clustered into time-dependent groups (nine clusters each in leaves and roots); gene functions were distributed evenly among the groups convergence. KEGG enrichment analysis showed the genes related to plant hormone signal transduction were enriched in almost all treatment comparisons. Under salt stress, genes belongs to PYL (abscisic acid receptor PYR / PYL family), PP2C (Type 2C protein phosphatases), GH3 (Gretchen Hagen3), ETR (ethylene receptor), EIN2/3 (ethylene-insensitive protein 2/3), JAZ (Genes such as jasmonate ZIM-domain gene) and MYC2 (Transcription factor MYC2) had extremely similar expression patterns. The results of qPCR of 12 randomly selected genes confirmed the accuracy of RNA-seq. Conclusions: Under the impact of high salinity (300mM) environment, Jerusalem artichoke in the seedling stage was difficult to survive for a long time, and the phenotype was severe in the short term. Based on the expression of genes on the time scale, we found that the distribution of gene functions in time is relatively even. Upregulation of the phytohormone signal transduction had a crucial role in the response of Jerusalem artichoke seedlings to salt stress, the genes of abscisic acid, auxin, ethylene, and jasmonic acid had the most obvious change pattern.

scholarly journals Comparative Transcriptomic Analysis Reveals the Effects of Drought on the Biosynthesis of Methyleugenol in Asarum sieboldii Miq.

Biomolecules ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1233
Author(s):  
Fawang Liu ◽  
Tahir Ali ◽  
Zhong Liu
Keyword(s):  
Drought Stress ◽  
Metabolic Pathways ◽  
Molecular Genetic ◽  
Volatile Oil ◽  
Perennial Herb ◽  
Rna Seq ◽  
The Family ◽  
Genetic Mechanisms ◽  
Effects Of Drought ◽  
Comparative Transcriptomic Analysis

Asarum sieboldii Miq., a perennial herb in the family Aristolochiaceae, is widely used to treat colds, fever, headache and toothache in China. However, little is known about the drought-tolerance characteristics of A. sieboldii. In this study, to elucidate the molecular–genetic mechanisms of drought-stress tolerance of A. sieboldii, RNA-seq was conducted. In total, 53,344 unigenes were assembled, and 28,715 unigenes were annotated. A total of 6444 differential-expression unigenes (DEGs) were found, which were mainly enriched in phenylpropanoid, starch and sucrose metabolic pathways. Drought stress revealed significant up-regulation of the unigenes encoding PAL, C4H, HCT, C3H, CCR and IGS in the methyleugenol-biosynthesis pathway. Under the condition of maintaining drought for 15 days and 30 days, drought stress reduced the biosynthesis of volatile oil by 24% and 38%, respectively, while the production of key medicinal ingredients (such as methyl eugenol) was increased. These results provide valuable information about the diverse mechanisms of drought resistance in the A. sieboldii, and the changes in the expression of the genes involved in methyleugenol biosynthesis in response to drought stress.

scholarly journals Identification of key modules and hub genes regulating drought stress response in rice drought sensitive line PY6 by weighted gene co-expression network analysis

2020 ◽  
Author(s):  
Baiyang Yu ◽  
Jianbin Liu ◽  
Di Wu ◽  
Ying Liu ◽  
Weijian Cen ◽  
...  
Keyword(s):  
Drought Stress ◽  
Network Analysis ◽  
Drought Resistance ◽  
Differentially Expressed ◽  
Chromosome 1 ◽  
Genetic Linkage Analysis ◽  
Rna Seq ◽  
Hub Genes ◽  
The Impact ◽  
Go Terms

Abstract Background: Drought stress is an adverse factor with deleterious effects on several facets of rice growth. However, the mechanism underlying drought resistance in rice remains unclear. In order to genetically understand the potential molecular mechanism for drought response in rice, a drought sensitive Chromosome Segment Substitution Line (CSSL) PY6, which was constructed by the introgression of genomic segments of drought sensitive variety LAMBAYEQUE1 into drought-resistance variety PR403 via backcrossing, was used to map the QTL locus dss-1 for its sensitive phenotype, and to reveal the impact of dss-1 on the transcriptional profiling of PY6 via RNA-seq and WGCNA (weighted gene co-expression network analysis) analysis. Results: The genetic linkage analysis showed that dss-1 was located on the short arm of chromosome 1 of rice. In contrast to PR403, the over-accumulation of H 2 O 2 and MDA that might result in drought sensitive phenotype was observed in PY6 under drought stress. In the analysis of RNA-seq data, the identified differentially expressed genes (DEGs) mainly enriched in photosynthesis-related GO terms and exhibited a down-regulation pattern of their expressions in both PY6 and PR403 in response to drought stress, indicating that the photosynthesis was greatly inhibited in rice. Further WGCNA analysis constructed a co-expression network with 26 gene modules in which 4 and 3 modules that were highly correlated with H 2 O 2 and MDA, respectively. Likewise, the GO analysis of the differentially expressed hub genes (DEHGs) enriched in H 2 O 2 -correlated modules showed that the photosynthesis related GO terms were consistently over-represented. Furthermore, functional annotation of DEHGs in H 2 O 2 and MDA correlated modules revealed a cross talk between abiotic and biotic stresses. This was reflected by the differential expression alterations of hub genes which were annotated as encoding MYBs, laccases, WRKYs, and PRs family proteins, and ZFP36 were notably observed between PY6 and PR403 in response drought stress. Conclusions: Collectively, we speculated that drought-induced the inhibition of photosynthesis lead to the accumulation of H 2 O 2 and MDA that can trigger the reprogramming the profiling of transcriptome in rice. This included the differential regulation of hub genes that involve in ROS eliminated pathways to prevent the damage of rice plants from oxidative stress.

scholarly journals Expression of Genes Related to Plant Hormone Signal Transduction in Jerusalem Artichoke (Helianthus tuberosus L.) Seedlings under Salt Stress

Agronomy ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 163
Author(s):  
Yang Yue ◽  
Jueyun Wang ◽  
Wencai Ren ◽  
Zhaosheng Zhou ◽  
Xiaohua Long ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Salt Stress ◽  
Salt Tolerance ◽  
Plant Hormone ◽  
Jerusalem Artichoke ◽  
Helianthus Tuberosus ◽  
Rna Seq ◽  
Tolerance Mechanisms ◽  
Expression Of Genes ◽  
Gene Functions

Background: Jerusalem artichoke (Helianthus tuberosus L.) is moderately tolerant to salinity stress and has high economic value. The salt tolerance mechanisms of Jerusalem artichoke are still unclear. Especially in the early stage of Jerusalem artichoke exposure to salt stress, gene transcription is likely to undergo large changes. Previous studies have hinted at the importance of temporal expression analysis in plant transcriptome research. Elucidating these changes may be of great significance to understanding the salt tolerance mechanisms of it. Results: We obtained high-quality transcriptome from leaves and roots of Jerusalem artichoke exposed to salinity (300 mM NaCl) for 0 h (hour), 6 h, 12 h, 24 h, and 48 h, with 150 and 129 unigenes and 9023 DEGs (differentially expressed genes). The RNA-seq data were clustered into time-dependent groups (nine clusters each in leaves and roots); gene functions were distributed evenly among them. KEGG enrichment analysis showed the genes related to plant hormone signal transduction were enriched in almost all treatment comparisons. Under salt stress, genes belonging to PYL (abscisic acid receptor PYR/PYL family), PP2C (Type 2C protein phosphatases), GH3 (Gretchen Hagen3), ETR (ethylene receptor), EIN2/3 (ethylene-insensitive protein 2/3), JAZ (genes such as jasmonate ZIM-domain gene), and MYC2 (Transcription factor MYC2) had extremely similar expression patterns. The results of qRT-PCR of 12 randomly selected and function known genes confirmed the accuracy of RNA-seq. Conclusions: Under the influence of high salinity (300 mM) environment, Jerusalem artichoke suffer serious damage in a short period of time. Based on the expression of genes on the time scale, we found that the distribution of gene functions in time is relatively even. Upregulation of the phytohormone signal transduction had a crucial role in the response of Jerusalem artichoke seedlings to salt stress, and the genes of abscisic acid, auxin, ethylene, and jasmonic acid had the most obvious change pattern. Research emphasized the regulatory role of hormones under high salt shocks and provided an explorable direction for the study of plant salt tolerance mechanisms.

Sign in / Sign up

Export Citation Format

Share Document